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Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in complex with AMP-PNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AUI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 291 25% PEG 6000, 0.1 M Sodium acetate pH 5.0, 0.1 M NaCl. Protein:precipitant ratio 2:1.
Protein buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 1 mM DTT, 10 mM AMP-PNP.
Crystal Properties Matthews coefficient Solvent content 2.44 49.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.958 α = 90 b = 61.958 β = 90 c = 95.924 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M KB focusing mirrors 2018-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979300 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.65 47.96 99.8 0.083 0.02 0.999 18.9 19 26240 27.77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 99.8 0.666 0.164 0.937 4.8 17.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7AUI 1.65 46.87 24867 1336 99.8 0.2106 0.209 0.2175 0.242 0.243 RANDOM 35.977
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.14 0.07 0.14 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.579 r_dihedral_angle_3_deg 13.725 r_dihedral_angle_4_deg 10.445 r_dihedral_angle_1_deg 6.796 r_angle_refined_deg 1.512 r_angle_other_deg 1.301 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_bond_other_d 0.007 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.579 r_dihedral_angle_3_deg 13.725 r_dihedral_angle_4_deg 10.445 r_dihedral_angle_1_deg 6.796 r_angle_refined_deg 1.512 r_angle_other_deg 1.301 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1158 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing Coot model building